CLEVELAND--NetGenics announced last week that biochemical pathways data from the Kyoto Encyclopedia of Genes and Genomes (KEGG), a public, multiorganism database developed by the Japanese Human Genome Program, will soon be added to NetGenics' Synergy framework. In addition to working collaboratively with the Kyoto group to integrate the database into Synergy, NetGenics will become a designated KEGG distributor and will provide funding to the Institute for Chemical Research at Kyoto University to support a postdoctoral researcher who will work on KEGG.
NetGenics's CEO Manuel Glynias told BioInform that incorporating KEGG into the Synergy platform will lend value to the database as a gene expression
analysis tool. "KEGG right now is a free service on the internet. Until it's integrated into a system like the one we're building, it's not as useful as it could be," Glynias said. Within Synergy, KEGG will be valuable as an analytical tool, not just as a browsing technology, he explained, adding, "We're taking what they did, which is a huge amount of work, and bringing value to it by integrating it into the world of bioinformatics a little better."
Specifically, Glynias said NetGenics is "building object-oriented wrappers" around KEGG so that it can be plugged into a CORBA program.
Glynias said the collection of pathway data will also be an important component of a gene expression product NetGenics is developing. "The idea is to be able to link sequences and expression data, but to link those with all the kinds of things we can know about sequences, including what pathways they're in as well as other kinds of things we know about gene properties," he said.
Explaining his company's long-range product plans, Glynias said, "What we really want to be able to do is take all the kinds of data that might be applicable to finding a drug faster and figure out a way that they can all talk to each other so you can ask complicated queries and bring all these kinds of data together to find candidate drugs faster."
For instance, Glynias said he envisions linking KEGG data to a chemical inventory. "A scientist can say, here's an interesting pathway that I'd love to be able to block with other drugs because it will give me a behavior in the cell that I want," he said, concluding, "The scientist can take all the little metabolites that we know are involved in this pathway and find any chemicals that we have in our million-chemical inventory that actually look like these and are chemically similar."
Demand for gene expression analysis software is growing among pharmaceutical researchers who are frustrated by not being able to decipher the vast amounts of data they are able to generate with DNA chips, Glynias said. "We were told by the folks at American Home Products that it could take two weeks for them to analyze results of an expression experiment. We think that is ridiculous. It's because the software isn't there yet," he explained, adding, "We think we can turn that into 10 minutes." KEGG, he said, "will be one of the important tools in getting us there."
Glynias described the gene expression data dilemma as an unsurprising obstacle in the path of genomics progress. "As soon as people got good at DNA sequencing there were tons of sequence and no ability to analyze it. Slowly the software has caught up and now we can analyze the data about as fast as it's generated. Now we're in the same sort of place with expression data, where you can make lots more data than you can possibly analyze," Glynias contended. "The software is catching up. A number of companies will be bringing out expression products," he observed, adding, "We think ours has some interesting wrinkles that others don't have and, as you can imagine, most of those are about integration."